MITSUTAKE AYORI

Structural and Computational Insights into Dynamics and Intermediate States of Orexin 2 Receptor Signaling.

Shun Yokoi, Ryoji Suno, Ayori Mitsutake

The journal of physical chemistry. B, May 9, 2024

Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.

Yutaka Maruyama, Ryo Igarashi, Yoshitaka Ushiku, Ayori Mitsutake

J. Chem. Inf. Model., 63(5) 1529-1541, Mar, 2023

Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature

Hiroshi Fujisaki, Hiromichi Suetani, Luca Maragliano, Ayori Mitsutake

Life, Aug 3, 2022

Computational Analysis of the SARS-CoV-2 RBD–ACE2-Binding Process Based on MD and the 3D-RISM Theory

Norio Yoshida, Yutaka Maruyama, Ayori Mitsutake, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov, Haruyuki Nakano

Journal of Chemical Information and Modeling, 62(11) 2889-2898, Jun 13, 2022

Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach

Yutaka Maruyama, Ayori Mitsutake

J, 5(1) 114-125, Feb 14, 2022

Molecular Dynamics Simulations for the Determination of the Characteristic Structural Differences between Inactive and Active States of Wild Type and Mutants of the Orexin2 Receptor.

Shun Yokoi, Ayori Mitsutake

The journal of physical chemistry. B, 125(17) 4286-4298, May 6, 2021

Universal Relation between Instantaneous Diffusivity and Radius of Gyration of Proteins in Aqueous Solution.

Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake, Ralf Metzler

Physical review letters, 126(12) 128101-128101, Mar 26, 2021

Mutation-induced change in chignolin stability from pi-turn to alpha-turn

Yutaka Maruyama, Shunpei Koroku, Misaki Imai, Koh Takeuchi, Ayori Mitsutake

RSC ADVANCES, 10(38) 22797-22808, Jun, 2020

Folding pathways of NuG2-a designed mutant of protein G-using relaxation mode analysis

Mitsutake Ayori, Takano Hiroshi

JOURNAL OF CHEMICAL PHYSICS, 151(4), Jul 28, 2019 Peer-reviewed

Identification of slow relaxation modes in a protein trimer via positive definite relaxation mode analysis

Karasawa Naoyuki, Mitsutake Ayori, Takano Hiroshi

JOURNAL OF CHEMICAL PHYSICS, 150(8), Feb 28, 2019 Peer-reviewed

Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory.

Yutaka Maruyama, Hiroshi Takano, Ayori Mitsutake

Biophysics and physicobiology, 16 407-429, 2019

Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates

Fujisaki Hiroshi, Moritsugu Kei, Mitsutake Ayori, Suetani Hiromichi

JOURNAL OF CHEMICAL PHYSICS, 149(13) 134112-134112, Oct 7, 2018 Peer-reviewed

Analysis of Structural Stability of Chignolin

Yutaka Maruyama, Ayori Mitsutake

Journal of Physical Chemistry B, 122(14) 3801-3814, Apr 12, 2018 Peer-reviewed

Relaxation mode analysis for molecular dynamics simulations of proteins

Ayori Mitsutake, Hiroshi Takano

Biophysical Reviews, 10(2) 375-389, Apr 1, 2018 Invited

Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy

Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenji Mochizuki, Kenichiro Koga

JOURNAL OF COMPUTATIONAL CHEMISTRY, 39(4) 202-216, Feb, 2018 Peer-reviewed

Dynamical Analysis Methods for Protein Folding Simulations

Mitsutake Ayori, Takano Hiroshi

BIOPHYSICAL JOURNAL, 114(3) 45A, Feb, 2018

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation

N. Karasawa, A. Mitsutake, H. Takano

PHYSICAL REVIEW E, 96(6), Dec, 2017 Peer-reviewed

Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT

Yutaka Maruyama, Ayori Mitsutake

JOURNAL OF PHYSICAL CHEMISTRY B, 121(42) 9881-9885, Oct, 2017 Peer-reviewed

Improved Relaxation Mode Analysis of a Hen Egg-White Lysozyme Protein

Naoyuki Karasawa, Ayori Mitsutake, Hiroshi Takano

BIOPHYSICAL JOURNAL, 112(3) 353A-353A, Feb, 2017

A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution

Tomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenichiro Koga

JOURNAL OF CHEMICAL PHYSICS, 144(22) 224104, Jun, 2016 Peer-reviewed

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